Hi Ryan,
On 08/05/2014 05:47 PM, Ryan C. Thompson wrote:
Hi again,
I'm looking at the examples in the summarizeOverlaps help page here:
http://www.bioconductor.org/packages/devel/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
And the examples fod preprocess.reads are a little
The man page '...' section was updated in GenomicAlignments 1.1.24 in
devel. I've now also updated it in 1.0.5 in release.
The '...' does not refer only to the fixed set of args listed below the
dots. The '...' encompasses any argument(s) provided to
summarizeOverlaps() not explicitly stated
Yes, I understand that the ... doesn't only refer to the fixed set of
arguments listed below. I was saying that the *documentation* for the
dots argument in summarizeOverlaps was actually talking about the below
arguments instead. I don't see it documented anywhere that the dots
arguments
Hi Valerie,
I got really busy around May and never got a chance to thank you for
adding this option to summarizeOverlaps! So thank you!
-Ryan
On Thu 01 May 2014 04:25:33 PM PDT, Valerie Obenchain wrote:
GenomicAlignments 1.1.8 has a 'preprocess.reads' argument. This should
be a function
Hi again,
I'm looking at the examples in the summarizeOverlaps help page here:
http://www.bioconductor.org/packages/devel/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
And the examples fod preprocess.reads are a little confusing. One of
the examples passes some additional ...
Thanks.
I have some concerns about the *ExtraArgs() functions. Passing flexible
args to findOverlaps in the existing mode functions fundamentally
changes the documented behavior. The modes were created to capture
specific overlap situations pertaining to gene features which are
graphically
Hi Valerie,
On Thu May 1 13:27:16 2014, Valerie Obenchain wrote:
I have some concerns about the *ExtraArgs() functions. Passing
flexible args to findOverlaps in the existing mode functions
fundamentally changes the documented behavior. The modes were created
to capture specific overlap
On 05/01/2014 02:05 PM, Ryan wrote:
Hi Valerie,
On Thu May 1 13:27:16 2014, Valerie Obenchain wrote:
I have some concerns about the *ExtraArgs() functions. Passing
flexible args to findOverlaps in the existing mode functions
fundamentally changes the documented behavior. The modes were
Hi all,
I recently asked about ways to do non-standard read counting in
summarizeOverlaps, and Martin Morgan directed me toward writing a custom
function to pass as the mode parameter. I have now written the custom
modes that I require for counting my ChIP-Seq reads, and I figured I
would
Hi Ryan,
These sound like great contributions. I didn't get an attachment - did
you send one?
Thanks.
Valerie
On 04/30/2014 01:06 PM, Ryan C. Thompson wrote:
Hi all,
I recently asked about ways to do non-standard read counting in
summarizeOverlaps, and Martin Morgan directed me toward
No, I forgot to attach the file. Here is the link:
https://www.dropbox.com/s/7qghtksl3mbvlsl/counting-modes.R
On Wed 30 Apr 2014 02:18:28 PM PDT, Valerie Obenchain wrote:
Hi Ryan,
These sound like great contributions. I didn't get an attachment - did
you send one?
Thanks.
Valerie
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